////////////////////////////////////////////////////////////////////// //// //// MEDIE - Semantic retrieval engine for MEDLINE //// ////////////////////////////////////////////////////////////////////// var NUM_PREFETCH_RESULTS = 20; var main_cgi_name = "search.cgi"; var query_cgi_name = "query.cgi"; var rungcl_cgi_name = "rungcl.cgi"; // old rungcl_cgi_name = "simplify.cgi"; var cgi1 = "completion.cgi"; // object, subject completion cgi var cgi2 = "verb.cgi"; // verb completion cgi var cgi3 = "title.cgi"; // journal title completion cgi var color = { backgroundSelected: "rgb( 5%, 5%, 5% )", // for completion foregroundSelected: "rgb( 99%, 99%, 99% )", // for completion background: "rgb( 99%, 99%, 99% )", // for completion foreground: "rgb( 10%, 10%, 10% )", // for completion type: "rgb( 40%, 40%, 40% )", // for completion id: "rgb( 45%, 45%, 70% )", // for completion border: "rgb( 30%, 30%, 30% )", // error: "rgb( 70%, 0%, 0% )", collation: "rgb( 30%, 30%, 30% )" } var months = { jan: 1, feb: 2, mar: 3, apr: 4, may: 5, jun: 6, jul: 7, aug: 8, sep: 9, oct: 10, nov: 11, dec: 12 }; var lowrank = 201; var publication_ranks = { "0370647": 1, "8309206": 2, "0255562": 3, "2985150R": 4, "101124168": 5, "0404511": 6, "101124169": 7, "100962782": 8, "0413066": 9, "0410462": 10, "9502015": 11, "0231714": 12, "100941354": 13, "9216904": 14, "7804039": 15, "9600627": 16, "2985213R": 17, "7501160": 18, "9604648": 19, "8006258": 20, "2985134R": 21, "7607088": 22, "100890575": 23, "100962779": 24, "101124171": 25, "101130617": 26, "101137067": 27, "9883513": 28, "0434624": 29, "9211097": 30, "0361046": 31, "101155473": 32, "0421737": 33, "8711660": 34, "9706653": 35, "9809671": 36, "8913428": 37, "7503089": 38, "9432918": 39, "7802877": 40, "9802571": 41, "8805125": 42, "101183755": 43, "101120028": 44, "100955717": 45, "7808616": 46, "8809320": 47, "101190261": 48, "2985109R": 49, "0117605": 50, "0335405": 51, "0372370": 52, "15040080R": 53, "0370600": 54, "7610674": 55, "8219702": 56, "0372351": 57, "0157313": 58, "0370475": 59, "0372435": 60, "0374630": 61, "101139309": 62, "8507085": 63, "8309333": 64, "9200566": 65, "0370121": 66, "9107782": 67, "0147763": 68, "7900832": 69, "9208688": 70, "0375356": 71, "100883395": 72, "101130150": 73, "101322263": 74, "9876465": 75, "8807282": 76, "7513292": 77, "2985151R": 78, "7906158": 79, "9302532": 80, "7505876": 81, "100966032": 82, "9518021": 83, "7603509": 84, "100911346": 85, "8208664": 86, "8902526": 87, "7808666": 88, "101125647": 89, "101088070": 90, "8302946": 91, "0372374": 92, "0271103": 93, "0144032": 94, "0376473": 95, "9890299": 96, "0370543": 97, "9107784": 98, "0047103": 99, "9111375": 100, "9607835": 101, "0372367": 102, "0117147": 103, "8301365": 104, "9708669": 105, "9885358": 106, "8900118": 107, "9612306": 108, "100973461": 109, "9009458": 110, "9421642": 111, "8209988": 112, "101213381": 113, "9111376": 114, "101165244": 115, "9811312": 116, "7702118": 117, "101231360": 118, "7905840": 119, "0370512": 120, "0372763": 121, "8605731": 122, "0372440": 123, "9815056": 124, "9010218": 125, "0376476": 126, "8103150": 127, "8310903": 128, "9215429": 129, "0370416": 130, "100957246": 131, "7805975": 132, "9437445": 133, "9208958": 134, "9604391": 135, "101137089": 136, "9421549": 137, "2985108R": 138, "1275002": 139, "100963049": 140, "2984705R": 141, "0372373": 142, "8701744": 143, "9431859": 144, "7707449": 145, "0411011": 146, "0372537": 147, "0372741": 148, "8102140": 149, "0401141": 150, "7806090": 151, "8903774": 152, "0370605": 153, "7503056": 154, "9711805": 155, "8006263": 156, "0376515": 157, "8502408": 158, "9013836": 159, "9001516": 160, "101300458": 161, "8710523": 162, "8109087": 163, "8804484": 164, "9505803": 165, "9207397": 166, "0372355": 167, "101128775": 168, "9100492": 169, "8711562": 170, "8510851": 171, "0213264": 172, "101190390": 173, "101215604": 174, "9310916": 175, "8704895": 176, "0404471": 177, "0052457": 178, "8610640": 179, "9201390": 180, "9203213": 181, "9607332": 182, "100883581": 183, "101300366": 184, "100939340": 185, "2985117R": 186, "100883691": 187, "7906255": 188, "0372354": 189, "9890633": 190, "8501455": 191, "0204634": 192, "8712028": 193, "9110718": 194, "9815369": 195, "0417353": 196, "9509184": 197, "9500160": 198, "0401224": 199, "9304532": 200 }; ////////////////////////////////////////////////////////////////////// //// //// Library //// ////////////////////////////////////////////////////////////////////// // manipulating HTML elements function showLayer( id ) { var elem = $( id ); elem.style.position = 'static'; elem.style.visibility = 'inherit'; elem.style.display = ''; elem.removeClassName('hidden'); } function hideLayer( id ) { var elem = $( id ); elem.style.position = 'absolute'; // elem.style.visibility = 'hidden'; elem.style.display = 'none'; } function showByClass( id ) { var elem = $( id ); elem.removeClassName('hidden'); elem.addClassName('visible'); } function hideByClass( id ) { var elem = $( id ); elem.removeClassName('visible'); elem.addClassName('hidden'); } function deleteChildren( doc ) { if ( ! doc ) { return; } if ( ! doc.childNodes ) { return; } while ( doc.childNodes.length > 0 ) { doc.removeChild( doc.firstChild ); } } function elementPosition( elem ) { var left = 0; var top = 0; var e = elem; while ( e ) { left += e.offsetLeft; top += e.offsetTop; e = e.offsetParent; } return { left: left, top: top }; } function windowPosition() { var position = { left: 0, right: 0, top: 0, bottom: 0 }; if ( document.all ) { position.left = document.body.scrollLeft; position.right = position.left + document.body.clientWidth; position.top = document.body.scrollTop; position.bottom = position.top + document.body.clientHeight; } else { position.left = pageXOffset; position.right = position.left + innerWidth; position.top = pageYOffset; position.bottom = position.top + innerHeight; } position.right = position.right - 20; position.bottom = position.bottom - 20; return position; } // HTTP client function createXMLHttpRequest() { if ( window.XMLHttpRequest ) { return new XMLHttpRequest(); } else { return new ActiveXObject( "Microsoft.XMLHTTP" ); } } function getTextValue(el) { return el.textContent ? el.textContent : el.text; } ////////////////////////////////////////////////////////////////////// //// //// table sorting //// ////////////////////////////////////////////////////////////////////// var target_texts; function sortTable( id, col, is_entity ) { var target_column = col; var tbody = $( id ).getElementsByTagName( "tbody" )[ 0 ]; var target_rows = tbody.getElementsByTagName( "tr" ); target_texts = new Array(); var row_ids = new Array(); var cells = new Array(); for ( var i = 0; i < target_rows.length; ++i ) { row_ids[ i ] = i; cells[ i ] = target_rows[ i ]; target_texts[ i ] = extractText( target_rows[ i ].getElementsByTagName( "td" )[ target_column ], is_entity ); if ( target_texts[ i ] == "" ) { target_texts[ i ] = "\xff"; // empty string should be put lower } } row_ids.sort( compareRows ); for ( var i = 0; i < target_rows.length; ++i ) { tbody.appendChild( cells[ row_ids[ i ] ] ); } } function extractText( elem, is_entity ) { var text = ""; var nodes = elem.childNodes; for ( var i = 0; i < nodes.length; ++i ) { if ( nodes[ i ].nodeType == 3 ) { // TEXT_NODE if ( ! is_entity ) { text = text + nodes[ i ].nodeValue.toLowerCase(); } } else if ( nodes[ i ].nodeType == 1 ) { // ELEMENT_NODE text = text + extractText( nodes[ i ], false ); } } return text; } function compareRows( a, b ) { var val_a = target_texts[ a ]; var val_b = target_texts[ b ]; if ( val_a < val_b ) { return -1; } if ( val_a > val_b ) { return 1; } return 0; } ////////////////////////////////////////////////////////////////////// //// //// coloring subject, verb, and object //// ////////////////////////////////////////////////////////////////////// var coloring = { subject: true, verb: true, object: true, gene: true, disease: true } function switchColoring( type ) { var name1, name2, isColoringOn; switch ( type ) { case "subject": coloring.subject = ! ( isColoringOn = coloring.subject ); break; case "verb" : coloring.verb = ! ( isColoringOn = coloring.verb ); break; case "object" : coloring.object = ! ( isColoringOn = coloring.object ); break; case "gene" : coloring.gene = ! ( isColoringOn = coloring.gene ); break; case "disease": coloring.disease = ! ( isColoringOn = coloring.disease ); break; } if ( isColoringOn ) { name1 = "." + type; name2 = "x" + type; } else { name1 = ".x" + type; name2 = type; } var elements = $$( name1 ); for ( var i=0; i window_position.right ) { position.left = window_position.right - width; } if ( position.left < window_position.left ) { position.left = window_position.left; } if ( position.top + popupWindow.offsetHeight > window_position.bottom ) { position.top = window_position.bottom - popupWindow.offsetHeight; } if ( position.top < window_position.top ) { position.top = window_position.top; } popupWindow.style.left = position.left + 'px'; popupWindow.style.top = position.top + 'px'; popupWindow.style.width = width + "px"; popupWindow.style.padding = "5px"; popupWindow.style.visibility = 'visible'; } function hidePopupWindow() { if ( popupWindow ) { popupWindow.style.visibility = 'hidden'; } } ////////////////////////////////////////////////////////////////////// //// //// Popup window for database links //// ////////////////////////////////////////////////////////////////////// // reform deleteChildren(), windowPosition() var PopupWindow = function( popupID ) { this.window = null; this.isActive = false; this.initialize = function() { if ( this.window ) { return; } var self = this; this.window = document.createElement( "div" ); this.window.id = popupID; this.window.className = "popup"; this.window.style.position = "absolute"; this.window.style.visibility = "hidden"; this.window.style.padding = "5px"; this.window.onmouseover = function () { self.isActive = true; }; this.window.onmouseout = function () { self.hide(); }; document.body.appendChild( this.window ); }; this.calcPos = function( target ) { var position = elementPosition( target ); position.top += target.offsetHeight; var wpos = windowPosition(); if ( position.left + this.window.offsetWidth > wpos.right ) { position.left = wpos.right - this.window.offsetWidth; } if ( position.left < wpos.left ) { position.left = wpos.left; } if ( position.top + this.window.offsetHeight > wpos.bottom ) { position.top = wpos.bottom - this.window.offsetHeight; } if ( position.top < wpos.top ) { position.top = wpos.top; } return position; }; this.append = function( arg ) { }; this.show = function( target, arg ) { this.isActive = true; $( this.window.id ).innerHTML = ""; this.append( arg ); var position = this.calcPos( target ); this.window.style.left = position.left + "px"; this.window.style.top = position.top + "px"; this.window.style.visibility = "visible"; }; this.hide = function() { if ( ! this.isActive ) { return; } this.isActive = false; var self = this; setTimeout( function() { self.hideNow(); }, 1000 ); }; this.hideNow = function() { if ( ! this.window || this.isActive ) { return; } this.window.style.visibility = "hidden"; deleteChildren( this.window ); }; this.initialize(); } var popupHelp; var dblinksPopup; function initPopups() { popupHelp = new PopupWindow( "popuphelp" ); popupHelp.append = function( text ) { this.window.style.width = "300px"; this.window.style.fontSize = "100%" ; $( this.window.id ).innerHTML = text; } dblinksPopup = new PopupWindow( "dblinks" ); dblinksPopup.speciesClassMap = { "Caenorhabditis elegans" : "org0", "Drosophila melanogaster" : "org1", "Homo sapiens" : "org2", "Mus musculus" : "org3", "Rattus norvegicus" : "org4", "Saccharomyces cereviciae" : "org5", "Schizosaccharomyces pombe" : "org6" }; dblinksPopup.append = function( node ) { var type = node.getAttribute( "type" ); var gene_id = node.getAttribute( "uniprot_id" ); var gene_symbol = node.getAttribute( "gene_symbol" ); var gene_name = node.getAttribute( "gene_name" ); var species = node.getAttribute( "species" ); var db_site = node.getAttribute( "db_site" ); var disease_id = node.getAttribute( "facta_id" ); type = ( type )? type : ""; gene_id = ( gene_id )? gene_id : ""; gene_symbol = ( gene_symbol )? gene_symbol : ""; gene_name = ( gene_name )? gene_name : ""; species = ( species )? species : ""; db_site = ( db_site )? db_site : ""; disease_id = ( disease_id )? disease_id : ""; var types = type.split(";"); var gene_ids = gene_id.split(";"); var gene_symbols = gene_symbol.split(";"); var gene_names = gene_name.split(";"); var speciess = species.split(";"); var db_sites = db_site.split(";"); var disease_ids = disease_id.split(";"); for ( var i = 0; i < types.length; ++i ) { if (types[i] == "gene" || types[i] == "gene_prod" || types[i] == "disease") { this.appendTitleNode( types[ i ], gene_symbols[ i ], speciess[ i ], disease_ids[ i ] ); this.appendLinkNode( db_sites[ i ] ); this.appendDiseaseIDNode( disease_ids[ i ] ); } } }; dblinksPopup.appendDiseaseIDNode = function( disease_id ) { var node = document.createElement( "div" ); node.appendChild( document.createTextNode( disease_id ) ); node.style.marginBottom = "2px"; this.window.appendChild( node ); }; dblinksPopup.appendTitleNode = function( type, gene_symbol, species, disease_id ) { // make gene/gene_prod/disease title var titleString; var titleNode = document.createElement( "div" ); titleNode.className = "db_title"; switch ( type ) { case "gene" : case "gene_prod" : titleString = gene_symbol + " (" + species + ")"; break; case "disease" : titleString = "disease"; break; } var speciesClass = this.speciesClassMap[ species ]; if ( speciesClass ) { titleNode.className = "db_title " + speciesClass; } else { titleNode.style.backgroundColor = "rgb( 70%, 70%, 70% )"; } titleNode.appendChild( document.createTextNode( titleString ) ); this.window.appendChild( titleNode ); }; dblinksPopup.appendLinkNode = function( db_site ) { var links = db_site.split( '|' ); for ( var i=0; i fiche.php // * HUGO: URL and CGI program name changed // * PIR: no longer serviced // * S.pombe: interface changed // case "GDB" : href = "http://www.gdb.org/gdb-bin/genera/genera/hgd/DBObject?!key=GDB%3A" + link[ 1 ] + "&!sub=0"; break; // case "GenAtlas" : href = "http://www.dsi.univ-paris5.fr/genatlas/fiche1.php?symbol=" + link[ 1 ] + "#carte"; break; // case "HUGO" : href = "http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id=" + link[ 1 ]; break; // case "PIR" : href = "http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?xref=1&id=" + link[ 1 ]; break; // case "S.pombe" : href = "http://www.genedb.org/genedb/Search?name=" + link[ 1 ] + "&organism=pombe"; break; case "Info-PubMed": href = INFO_PUBMED_URL; onclick = new Function( "", "addToInfoPubMed( \"" + link[ 1 ] + "\", 1 ); return false;" ); break; case "EntrezGene" : href = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=" + link[ 1 ]; break; case "FlyBase" : href = "http://www.flybase.org/.bin/fbidq.html?" + link[ 1 ]; break; case "GenAtlas" : href = "http://www.dsi.univ-paris5.fr/genatlas/fiche.php?symbol=" + link[ 1 ] + "#carte"; break; case "HUGO" : href = "http://www.genenames.org/data/hgnc_data.php?hgnc_id=" + link[ 1 ]; break; case "MGI" : href = "http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI:" + link[ 1 ]; break; case "MIPS" : href = "http://mips.gsf.de/genre/proj/yeast/searchEntryAction.do?text=" + link[ 1 ]; break; case "OMIM" : href = "http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=" + link[ 1 ]; break; case "RGD" : href = "http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=" + link[ 1 ]; break; case "S.pombe" : href = "http://www.genedb.org/genedb/Dispatcher?formType=navBar&organism=All%3A*&desc=yes&submit=Search&name=" + link[ 1 ]; break; case "SGD" : href = "http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=" + link[ 1 ]; break; case "SWISS-PROT" : href = "http://www.expasy.ch/cgi-bin/niceprot.pl?" + link[ 1 ]; break; case "TrEMBL" : href = "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[SPTREMBL-acc:" + link[ 1 ] + "]+-vn+2"; break; case "WormBase" : href = "http://www.wormbase.org/db/gene/gene?name=" + link[ 1 ] + ";class=CDS"; break; case "UMLS" : href = "http://www.nlm.nih.gov/research/umls/"; /* temporary */ break; } // XXX: just skip unknown lable // if ( ! href ) { return; } if ( ! href ) { continue; } var a = document.createElement( "a" ); a.href = href; a.appendChild( document.createTextNode( label ) ); a.target = "_blank"; if ( onclick ) { a.onclick = onclick; } var linkNode = document.createElement( "div" ); linkNode.style.marginBottom = "2px"; linkNode.appendChild( a ); this.window.appendChild( linkNode ); } }; } ////////////////////////////////////////////////////////////////////////////////////////////////////////// var dblink_popup = null; var dblink_popup_active = false; var dblink_class_map = { "Caenorhabditis elegans" : "org0", "Drosophila melanogaster" : "org1", "Homo sapiens" : "org2", "Mus musculus" : "org3", "Rattus norvegicus" : "org4", "Saccharomyces cereviciae" : "org5", "Schizosaccharomyces pombe" : "org6" }; var sendto_popup = null; var sendto_popup_active = false; function showSendTo( event, target, symbol, id ) { if ( ! sendto_popup ) { sendto_popup = document.createElement( "div" ); sendto_popup.style.position = "absolute"; sendto_popup.style.visibility = "hidden"; document.body.appendChild( sendto_popup ); } deleteChildren( sendto_popup ); var sendToObject = document.createElement( "div" ); sendToObject.appendChild( document.createTextNode( "send to object field" ) ); var funcObject = "var field = $( 'object' );" + "var newText = field.value + ' [" + symbol + "]';" + "field.value = newText;" + "oc.last = newText;" + "oc.dict.push( { symbol: '[" + symbol + "]', id: '" + id + "' } );"; sendToObject.onclick = new Function( "", funcObject ); sendto_popup.appendChild( sendToObject ); var sendToSubject = document.createElement( "div" ); sendToSubject.appendChild( document.createTextNode( "send to subject field" ) ); var funcSubject = "var field = $( 'subject' );" + "var newText = field.value + ' [" + symbol + "]';" + "field.value = newText;" + "sc.last = newText;" + "sc.dict.push( { symbol: '[" + symbol + "]', id: '" + id + "' } );"; sendToSubject.onclick = new Function( "", funcSubject ); sendto_popup.appendChild( sendToSubject ); sendto_popup.className = 'popup'; sendto_popup.onmouseover = function () { sendto_popup_active = true; }; sendto_popup.onmouseout = function () { removeSendTo(); }; sendto_popup_active = true; dblink_popup_active = true; var position = elementPosition( target ); position.top += target.offsetHeight; var window_position = windowPosition(); if ( position.left + sendto_popup.offsetWidth > window_position.right ) { position.left = window_position.right - sendto_popup.offsetWidth; } if ( position.left < window_position.left ) { position.left = window_position.left; } if ( position.top + sendto_popup.offsetHeight > window_position.bottom ) { position.top = window_position.bottom - sendto_popup.offsetHeight; } if ( position.top < window_position.top ) { position.top = window_position.top; } sendto_popup.style.left = position.left + 'px'; sendto_popup.style.top = position.top + 'px'; sendto_popup.style.visibility = 'visible'; } function removeSendToNow() { if ( sendto_popup && ! sendto_popup_active ) { sendto_popup.style.visibility = 'hidden'; } } function removeSendTo() { if ( sendto_popup_active ) { sendto_popup_active = false; setTimeout( 'removeSendToNow()', 1000 ); } } function removeDbLinksNow() { if ( dblink_popup && ! dblink_popup_active ) { dblink_popup.style.visibility = 'hidden'; } } function removeDbLinks() { if ( dblink_popup_active ) { dblink_popup_active = false; setTimeout( 'removeDbLinksNow()', 1000 ); } } function createInfoPubmedLink( id ) { var a = document.createElement( "a" ); a.href = INFO_PUBMED_URL + "?symbolquery=" + id; a.target = "_blank"; a.appendChild( document.createTextNode( "Info-PubMed" ) ); var div = document.createElement( "div" ); div.className = "item"; div.appendChild( document.createTextNode( "See" ) ); div.appendChild( a ); return div; } function addToInfoPubMed( str, tox ) { var info_pubmed_request = createXMLHttpRequest(); if ( info_pubmed_request ) { info_pubmed_request.onreadystatechange = function () { openInfoPubMed( info_pubmed_request ); }; var postdata; if ( tox == 1 ) { postdata = "targetfor=1&addable=1&ent1=" + escape( str ) + "&mems=ent1"; } else { postdata = "targetfor=1&addable=1&ent2=" + escape( str ) + "&mems=ent2"; } info_pubmed_request.open( "POST", INFO_PUBMED_URL + "SessionMem", true ); info_pubmed_request.setRequestHeader( "Content-Type", "application/x-www-form-urlencoded" ); info_pubmed_request.send( postdata ); } } var info_pubmed_window = null; function openInfoPubMed( info_pubmed_request ) { if ( info_pubmed_request && info_pubmed_request.readyState == 4 ) { if ( info_pubmed_request.status != 200 ) { alert( "Info-PubMed is not working now." ); } else { if ( ! info_pubmed_window || info_pubmed_window.closed ) { if ( window.opener && ! window.opener.closed && window.opener.name == "info_pubmed" ) { info_pubmed_window = opener; } else { info_pubmed_window = window.open( INFO_PUBMED_URL, "info_pubmed" ); } } else { info_pubmed_window.location.reload(); } } } } ////////////////////////////////////////////////////////////////////// //// //// Result Formatting //// ////////////////////////////////////////////////////////////////////// function isCommaEtc( doc ) { if ( !doc || !doc.childNodes ) { return; } var child = doc.childNodes[ 0 ]; if ( child.nodeType == 3 ) { // TEXT_NODE switch ( child.nodeValue ) { case "," : case "." : case ":" : case ";" : return true; default : return false; } } return false; } function setPopupEventHandlers(span, entityNode) { var origTitle = span.title; span.onclick = function() { span.title = ""; dblinksPopup.show( this, entityNode ); return false; }; span.onmouseout = function() { span.title = origTitle; dblinksPopup.hide(); return false; }; } function findMarkupClass(elem, variable) { var id = elem.getAttribute( "id" ); // if coloring, class="subject", else, class="xsubject" switch ( id ) { case variable[ "$subject" ]: return coloring.subject ? "subject" : "xsubject"; case variable[ "$verb" ]: return coloring.verb ? "verb" : "xverb"; case variable[ "$object" ]: return coloring.object ? "object" : "xobject"; case variable[ "$keyword1" ]: return "keyword1"; case variable[ "$keyword2" ]: return "keyword2"; case variable[ "$keyword3" ]: return "keyword3"; case variable[ "$keyword4" ]: return "keyword4"; case variable[ "$keyword5" ]: return "keyword5"; case variable[ "$keyword6" ]: return "keyword6"; case variable[ "$keyword7" ]: return "keyword7"; case variable[ "$keyword8" ]: return "keyword8"; case variable[ "$keyword9" ]: return "keyword9"; case variable[ "$keyword10" ]: return "keyword10"; } if (variable[ "$ev_trigger" ] && variable[ "$ev_trigger" ][ id ]) { return "event-trigger"; } else if (variable[ "$ev_arg" ] && variable[ "$ev_arg" ][ id ]) { return "event-argument"; } else if (variable[ "$ev_part" ] && variable[ "$ev_part" ][ id ]) { return "event-participant"; } return null; } function convertResultText( doc, ret, variable ) { if ( !doc || !doc.childNodes ) { return; } for ( var i = 0; i < doc.childNodes.length; ++i ) { var child = doc.childNodes[ i ]; if ( child.nodeType == 3 ) { // TEXT_NODE ret.appendChild( document.createTextNode( child.nodeValue ) ); } else if ( child.nodeType == 1 ) { // ELEMENT_NODE if ( child.tagName == "entity_name" ) { // always markup var node = child; var span = document.createElement( "span" ); var type = node.getAttribute( "type" ); if ( type.search(/(^|;)gene(_prod)?(;|$)/) != -1 ) { span.className = coloring.gene ? "gene" : "xgene"; span.title = "click to popup database links"; setPopupEventHandlers(span, node); } else if ( type.search(/(^|;)disease(;|$)/) != -1 ) { span.className = coloring.disease ? "disease" : "xdisease"; span.title = "click to popup database links"; setPopupEventHandlers(span, node); } else { // do nothing for other named entity types } var markupClass = findMarkupClass( node, variable ); if ( markupClass ) { span.className += " " + markupClass; } if ( child.getAttribute( "class" ) ) { span.className += " " + child.getAttribute( "class" ); } convertResultText( child, span, variable ); ret.appendChild( span ); } else { // other tags var markupClass = findMarkupClass( child, variable ); if ( markupClass ) { // need a span for highlighting var span = document.createElement( "span" ); if ( child.getAttribute( "class" ) ) { span.className = child.getAttribute( "class" ) + " " + markupClass; } else { span.className = markupClass; } // NOTE: matuzaki: for what? if ( child.getAttribute( "title" ) ) { span.title = child.getAttribute( "title" ); } convertResultText( child, span, variable ); ret.appendChild( span ); } else { // just go down convertResultText( child, ret, variable ); } } } } } function appendXMLLink( parent, position, sentence_id, title, text ) { if ( !text ) text = sentence_id ? "\xbbsXML" : "\xbbXML"; if ( !title ) title = sentence_id ? "See linguistic annotations for the sentence" : "See linguistic annotations for the article"; parent.appendChild( document.createTextNode( " " ) ); var a = document.createElement( "a" ); var url = "showxml.cgi?position=" + position; if ( sentence_id ) url += "&sentence_id=" + sentence_id; a.href = url; a.target = "_blank"; a.title = title; a.className = "tiny_option"; a.appendChild( document.createTextNode( text ) ); parent.appendChild( a ); } function createTitleNode( result, id, variable ) { var title = result.getElementsByTagName( "ArticleTitle" )[ 0 ]; var title_text = document.createElement( "span" ); if ( title ) { convertResultText( title, title_text, variable ); } else { title_text.appendChild( document.createTextNode( "[No Title]" ) ); } var title_node = document.createElement( "span" ); title_node.className = "result_title"; var pmid = result.getElementsByTagName( "PMID" )[ 0 ].firstChild.nodeValue; if ( pmid ) { var a = document.createElement( "a" ); a.href = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=" + pmid; a.target = "_blank"; a.title = "Go to PubMed"; a.appendChild( title_text ); title_node.appendChild( a ); } else { title_node.appendChild( title_text ); } var position = result.getElementsByTagName( "position" )[ 0 ].firstChild.nodeValue; if ( position ) { appendXMLLink( title_node, position ); } return title_node; } function createCollationNode( result ) { var year = null; var journalTitle = "[journal title not available]"; var volume = null; var issue = null; var pmid = null; var pp = null; var authors = []; var collationNode = document.createElement( "div" ); // get year var pubDate = result.getElementsByTagName( "PubDate" ); if ( pubDate && 0 < pubDate.length ) { pubDate = pubDate[ 0 ]; var y = pubDate.getElementsByTagName( "Year" ); if ( y && 0 < y.length ) { year = y[ 0 ].firstChild.nodeValue; } } // get journal title var jt = result.getElementsByTagName( "Title" ); if ( jt && 0 < jt.length ) { journalTitle = jt[ 0 ].firstChild.nodeValue; } // get volume and issue var journal = result.getElementsByTagName( "Journal" ); if ( journal && journal.length ) { journal = journal[ 0 ]; var volumeNodes = journal.getElementsByTagName( "Volume" ); var issueNodes = journal.getElementsByTagName( "Issue" ); volume = ( volumeNodes && 0 < volumeNodes.length )? ( volumeNodes[ 0 ].firstChild.nodeValue ) : ( "" ); issue = ( issueNodes && 0 < issueNodes.length ) ? ( issueNodes[ 0 ].firstChild.nodeValue ) : ( "" ); } // get PubMedID var pmidNodes = result.getElementsByTagName( "PMID" ); if ( pmidNodes && 0 < pmidNodes.length ) { pmid = pmidNodes[0].firstChild.nodeValue; } // get pages var ppNodes = result.getElementsByTagName( "MedlinePgn" ); pp = ( ppNodes && 0 < ppNodes.length )? ( ppNodes[ 0 ].firstChild.nodeValue ) : ""; // get authors var authorListNodes = result.getElementsByTagName( "AuthorList" ); if ( authorListNodes && 0 < authorListNodes.length ) { var authorNodes = authorListNodes[0].getElementsByTagName( "Author" ); var firstName = ""; var lastName = ""; for ( var i=0; i"; // if we need debugging, uncomment this, then use FireBug try { console.log(message); } catch(x) { // not debugging } } ////////////////////////////////////////////////////////////////////// //// //// Search //// ////////////////////////////////////////////////////////////////////// var Search = function() { this.runGCLRequest = null; this.gclOptions = null; this.viewOptions = { outputFormat: "sentence", numberOfResults: 10 }; this.displayPosition = { start: 0, end: 0 }; this.resultsWindow = { sentence: null, article: null, table: null }; this.formData = null; this.results = null; this.summary = null; this.isSearchFinished = null; this.targetVariables = null; this.searchPosition = null; this.summaryStrings = null; this.submittedQuery = ""; this.time = 0; this.displayError = function( text ) { var summary_window = $( "results_summary" ); if ( summary_window ) { summary_window.className = "result_summary"; } var summary_num = $( "results_summary_num" ); if ( summary_num ) { deleteChildren( summary_num ); var span = document.createElement( "span" ); span.className = "item"; span.appendChild( document.createTextNode( "Error: " ) ); summary_num.appendChild( span ); summary_num.appendChild( document.createTextNode( text ) ); } showLayer( "results_field" ); }, this.editGCLQuery = function() { var element = $( "results_submitted_query_value" ); var field = '" + "
"; Element.update( element, field ); element.title = "edit GCL query"; element.onclick = ""; }, this.gclRun = function() { debug( "GCL search" ); this.initSearch(); $( "textarea" ).value = $( "textarea" ).value.replace( /\n/g, "" ); $( "textarea" ).value = $( "textarea" ).value.replace( /\s+/g, " " ); this.submittedQuery = $( "textarea" ).value; // and targets and summary ... pa this.targetVariables = [ "subject", "verb", "object" ]; this.displayResults( true ); }, this.getEndPosition = function() { // get end_position if ( this.viewOptions.numberOfResults < 0 ) { // negative values means all results return this.results.length; } return Math.min( this.displayPosition.start + this.viewOptions.numberOfResults , this.results.length ); }, this.getTbodyNode = function() { // wrapping of this.getPrevNextNode() var tbody = document.createElement( "tbody" ); var doc = document.createElement( "tr" ); tbody.appendChild( doc ); var td = document.createElement( "td" ); doc.appendChild( td ); td.setAttribute( "colSpan", 3 ); var node = this.underline( this.getPrevNextNode() ); td.appendChild( node ); var docx = document.createElement( "tr" ); tbody.appendChild( docx ); var tdx = document.createElement( "td" ); docx.appendChild( tdx ); tdx.setAttribute( "colSpan", 3 ); tdx.style.padding = "10px"; return tbody; }; this.overline = function( node ) { node.style.borderTop = "double 3px " + color.border; node.style.paddingTop = "3px"; return node; }; this.underline = function( node ) { node.style.borderBottom = "double 3px " + color.border; node.style.paddingBottom = "3px"; return node; }; this.displayResults = function( init ) { // display search results if ( ! this.gclOptions ) return; // when called without search var end_position = this.getEndPosition(); // display summary this.displaySummary( end_position, init ); if ( ! this.resultsWindow.sentence ) { this.initDisplay(); } // I'm not sure this is the right place to do this. // TODO: rename the ID of the
tag later showLayer("resultsField"); // add new results if ( this.displayPosition.end < end_position ) { for ( var i = this.displayPosition.end; i < end_position; ++i ) { var index = ( i >= this.sortperm.length ) ? i : this.sortperm[ i ][ 0 ]; var result = this.results[ index ]; var result_id = "result_" + index; // variable such as $vert = t1596 var variable = $H(); $A( result.getElementsByTagName( "variable" ) ).each( function( e, i ) { var varElement = e.getElementsByTagName( "var" )[ 0 ]; var valElement = e.getElementsByTagName( "value" )[ 0 ]; if ( varElement.firstChild && valElement.firstChild ) { var ev_var = varElement.firstChild.nodeValue.match( /\$ev_part|\$ev_arg|\$ev_trigger/ ); if ( ev_var ) { if ( ! variable[ ev_var ] ) variable[ ev_var ] = {}; variable[ ev_var ][ valElement.firstChild.nodeValue ] = varElement.firstChild.nodeValue; } else { variable[ varElement.firstChild.nodeValue ] = valElement.firstChild.nodeValue; } } } ); var position = result.getElementsByTagName( "position" )[ 0 ].firstChild.nodeValue; var sentence_id = variable[ "$sentence" ]; { // table if ( this.resultsWindow.table.childNodes.length == 0 ) { var prevNext = this.underline( this.getPrevNextNode() ); var node = this.resultsWindow.table.parentNode.parentNode.childNodes[ 0 ]; this.resultsWindow.table.parentNode.parentNode.insertBefore( prevNext, node ); } var doc = document.createElement( "tr" ); doc.id = result_id; var title = createTitleNode( result, result_id, variable ); var td1 = document.createElement( "td" ); td1.style.padding = "5px"; if ( title ) { td1.appendChild( title ); } appendXMLLink( td1, position, sentence_id ); doc.appendChild( td1 ); var tags = [].concat( $A( result.getElementsByTagName( "cons" ) ), $A( result.getElementsByTagName( "tok" ) ), $A( result.getElementsByTagName( "event_expression" ) ), $A( result.getElementsByTagName( "entity_name" ) ), $A( result.getElementsByTagName( "Event" ) ), $A( result.getElementsByTagName( "Trigger" ) ) ); if ( tags.length > 0 ) { var phrase_table = new Array(); for ( var j = 0; j < tags.length; ++j ) { var phrase = tags[ j ]; var td = document.createElement( "td" ); td.style.padding = "5px"; if ( variable[ "$ev_trigger" ] && variable[ "$ev_trigger" ][ phrase.getAttribute( "id" ) ] ) { var varName = variable[ "$ev_trigger" ][ phrase.getAttribute( "id" ) ]; td.className = "event-trigger"; phrase_table[ varName ] = td; } else if ( variable[ "$ev_arg" ] && variable[ "$ev_arg" ][ phrase.getAttribute( "id" ) ] ) { var varName = variable[ "$ev_arg" ][ phrase.getAttribute( "id" ) ]; td.className = "event-argument"; phrase_table[ varName ] = td; } else if ( variable[ "$ev_part" ] && variable[ "$ev_part" ][ phrase.getAttribute( "id" ) ] ) { var varName = variable[ "$ev_part" ][ phrase.getAttribute( "id" ) ]; td.className = "event-participant"; phrase_table[ varName ] = td; } else { switch ( phrase.getAttribute( "id" ) ) { case variable[ "$verb" ] : td.className = "verb" ; break; case variable[ "$object" ] : td.className = "object" ; break; case variable[ "$subject" ] : td.className = "subject" ; break; case variable[ "$keyword1" ] : td.className = "keyword1" ; break; case variable[ "$keyword2" ] : td.className = "keyword2" ; break; case variable[ "$keyword3" ] : td.className = "keyword3" ; break; case variable[ "$keyword4" ] : td.className = "keyword4" ; break; case variable[ "$keyword5" ] : td.className = "keyword5" ; break; case variable[ "$keyword6" ] : td.className = "keyword6" ; break; case variable[ "$keyword7" ] : td.className = "keyword7" ; break; case variable[ "$keyword8" ] : td.className = "keyword8" ; break; case variable[ "$keyword9" ] : td.className = "keyword9" ; break; case variable[ "$keyword10" ]: td.className = "keyword10"; break; } phrase_table[ td.className ] = td; } convertResultText( phrase, td, variable ); } for ( var j = 0; j < this.targetVariables.length; ++j ) { var target = phrase_table[ this.targetVariables[ j ] ]; if ( target ) { doc.appendChild( target ); } else { var td = document.createElement( "td" ); td.className = this.targetVariables[ j ]; td.appendChild( document.createTextNode( "" ) ); doc.appendChild( td ); } } } this.resultsWindow.table.appendChild( doc ); } { // article if ( this.resultsWindow.article.childNodes.length == 0 ) { this.resultsWindow.article.appendChild( this.getTbodyNode() ); } var tr1 = document.createElement( "tr" ); var tr2 = document.createElement( "tr" ); var td1 = document.createElement( "td" ); var td2 = document.createElement( "td" ); var td3 = document.createElement( "td" ); var tdx = document.createElement( "td" ); // for abstract tdx.setAttribute( "colSpan", 2 ); td3.id = result_id; td1.style.verticalAlign = "top"; td1.style.padding = "3px"; td2.style.verticalAlign = "top"; td2.style.padding = "3px"; td3.style.padding = "3px 3px 10px 3px"; td1.appendChild( document.createTextNode( i + 1 + "." ) ); // number var title = createTitleNode( result, result_id, variable ); if ( title ) { td3.appendChild( title ); } var collation = createCollationNode( result ); if ( collation ) { td3.appendChild( collation ); } var content = result.getElementsByTagName( "AbstractText" )[ 0 ]; var div = document.createElement( "div" ); div.className = "result_content"; if ( content ) { convertResultText( content, div, variable ); } else { div.innerHTML = '
No abstract available
'; } td3.appendChild( div ); appendXMLLink( div, position, sentence_id ); tr1.appendChild( td1 ); tr1.appendChild( td3 ); tr1.appendChild( td2 ); tr2.appendChild( document.createElement( "td" ) ); tr2.appendChild( tdx ); var tbody = document.createElement( "tbody" ); tbody.appendChild( tr1 ) //tbody.appendChild( tr2 ) this.resultsWindow.article.appendChild( tbody ); } { // sentence if ( this.resultsWindow.sentence.childNodes.length == 0 ) { this.resultsWindow.sentence.appendChild( this.getTbodyNode() ); } var doc = document.createElement( "tr" ); var td1 = document.createElement( "td" ); var td2 = document.createElement( "td" ); var td3 = document.createElement( "td" ); doc.appendChild( td1 ); doc.appendChild( td3 ); doc.appendChild( td2 ); td3.id = result_id; td1.style.verticalAlign = "top"; td1.style.padding = "3px"; td2.style.verticalAlign = "top"; td2.style.padding = "3px"; td3.style.padding = "3px 3px 15px 3px"; td1.appendChild( document.createTextNode( i + 1 + "." ) ); // number var title = createTitleNode( result, result_id, variable ); if ( title ) { td3.appendChild( title ); } var collation = createCollationNode( result ); if ( collation ) { td3.appendChild( collation ); } var sentence = $A( result.getElementsByTagName( "sentence" ) ).find( function( e, i ) { if ( sentence_id == e.getAttribute( "id" ) ) { return true; } return false; } ); if ( sentence ) { // if the sentence is equal to the title, do not display it if ( sentence.parentNode.tagName != "ArticleTitle" ) { var content_node = document.createElement( "div" ); content_node.className = "result_content"; convertResultText( sentence, content_node, variable ); appendXMLLink( content_node, position, sentence_id ); td3.appendChild( content_node ); } else { appendXMLLink( td3, position, sentence_id ); } } else { // no phrase tag, in keyword search var ne = result.getElementsByTagName( "named_entity" )[ 0 ]; if ( ne ) { // instead of phrase var ne_parent = ne.parentNode; if ( sentence = ne_parent ) { // not a bug if ( ne_parent.nodeName == "sentence" || ( ( sentence = ne_parent.parentNode ) && ne_parent.parentNode.nodeName == "sentence" ) ) { var content_node = document.createElement( "div" ); content_node.className = "result_content"; convertResultText( sentence, content_node, variable ); doc.appendChild( content_node ); } } } } var tbody = document.createElement( "tbody" ); tbody.appendChild( doc ) this.resultsWindow.sentence.appendChild( tbody ); } } this.displayPosition.end = end_position; } if ( init ) { this.runAgain(); } else if ( this.searchPosition ) { //this.showNext( Math.max( this.displayPosition.start - this.viewOptions.numberOfResults , 0 ) ); var limit = this.displayPosition.start + this.viewOptions.numberOfResults + NUM_PREFETCH_RESULTS; if ( this.viewOptions.numberOfResults < 0 || this.results.length < limit ) { this.runAgain( 'position', this.searchPosition ); } } }; this.getPrevNextNode = function() { var container = document.createElement( "div" ); if ( this.displayPosition.start > 0 ) { // show prev var proxy = this; var a = document.createElement( "a" ); a.style.textDecoration = "none"; a.href = ""; a.title = "show previous " + String( this.viewOptions.numberOfResults ) + " results"; a.onclick = function () { proxy.showNext( Math.max( proxy.displayPosition.start - proxy.viewOptions.numberOfResults , 0 ) ); return false; }; a.appendChild( document.createTextNode( "\xab show prev" ) ); container.appendChild( a ); container.appendChild( document.createTextNode( " | " ) ); } debug( "displayPosition.end = " + this.displayPosition.end ); debug( "displayPosition.start = " + this.displayPosition.start ); debug( "viewOptions.numberOfResults = " + this.viewOptions.numberOfResults ); debug( "results.length = " + this.results.length ); //if ( this.results.length < this.viewOptions.numberOfResults ) { // show next var proxy = this; var a = document.createElement( "a" ); a.style.textDecoration = "none"; a.href = ""; a.title = "show next " + String( this.viewOptions.numberOfResults ) + " results"; a.onclick = function () { proxy.showNext( proxy.getEndPosition() ); return false; }; a.appendChild( document.createTextNode( "show next \xbb" ) ); container.appendChild( a ); //} return container; }; this.getSummarySub = function( endPosition ) { var summary = null; if ( endPosition == this.results.length && this.isSearchFinished ) { summary = this.isSearchFinished; } else if ( this.viewOptions.numberOfResults < 0 || this.displayPosition.end < this.displayPosition.start + this.viewOptions.numberOfResults ) { summary = this.summary[ endPosition - 1 ]; } return summary; }; this.stopSearch = function() { var searching = $('searching'); if (searching) { searching.innerHTML = 'Search stopped.'; } if (this.runGCLRequest) { this.runGCLRequest.abort(); } }; this.displaySummary = function( end_position, init ) { var summary; if ( init ) { var summary_window = $( "results_summary" ); if ( summary_window ) { summary_window.className = "result_summary " } // show results field var field_name = "results_field" ; var field = $( field_name ); if ( field ) showLayer( field_name ); summary = null; } else if ( end_position == this.results.length && this.isSearchFinished ) { summary = this.isSearchFinished; } else if ( this.viewOptions.numberOfResults < 0 ) { summary = this.summary[ end_position - 1 ]; } else if ( this.displayPosition.end < this.displayPosition.start + this.viewOptions.numberOfResults ) { summary = this.summary[ end_position - 1 ]; } else { return; // no update } var summary_num = $( "results_summary_num" ); if ( summary_num ) { deleteChildren( summary_num ); if ( init || ( ( this.viewOptions.numberOfResults < 0 || end_position < this.displayPosition.start + this.viewOptions.numberOfResults ) && summary.next ) ) { var searching = document.createElement( "div" ); searching.id = "searching"; searching.style.whiteSpace = "nowrap"; searching.className = "searching"; summary_num.appendChild( searching ); searching.innerHTML = ' Searching'; } if ( summary ) { if ( summary.error ) { // Error this.displayError( summary.error.firstChild.nodeValue ); } else { // Keyword summary if ( this.isSearchFinished || this.displayPosition.start < end_position ) { var span = document.createElement( "span" ); span.className = "item"; if ( this.isSearchFinished && this.displayPosition.start == end_position ) { hideLayer( "resultsField" ); var span = document.createElement( "span" ); span.appendChild( document.createTextNode( "No results " ) ); span.style.fontWeight = "bold"; span.style.fontSize = "20px"; span.style.color = color.error; summary_num.appendChild( span ); } else if ( this.displayPosition.start + 1 == end_position ) { summary_num.appendChild( document.createTextNode( "Result " ) ); span.appendChild( document.createTextNode( end_position ) ); } else if ( this.displayPosition.start < end_position ) { summary_num.appendChild( document.createTextNode( "Results " ) ); span.appendChild( document.createTextNode( ( this.displayPosition.start + 1 ) + "-" + end_position ) ); } summary_num.appendChild( span ); if ( this.summaryStrings.length > 0 ) { var span = document.createElement( "span" ); span.className = "item"; span.appendChild( document.createTextNode( this.summaryStrings.join( ' ' ) ) ); //var string = $( "subject" ).value + " " + // $( "verb" ).value + " " + // $( "object" ).value; //span.appendChild( document.createTextNode( string ) ); summary_num.appendChild( document.createTextNode( " for " ) ); summary_num.appendChild( span ); } } } // timeout var timeout = summary.timeout; if ( timeout ) { summary_num.appendChild( document.createTextNode( " (Timeout in " + timeout.firstChild.nodeValue + " seconds)" ) ); } } // when summary exists // show "<< previous" and "next >>" if ( this.viewOptions.numberOfResults >= 0 ) { deleteChildren( $( "bottom_summary" ) ); $( "bottom_summary" ).appendChild( this.overline( this.getPrevNextNode() ) ); } } // Search time var summary_time = $( "results_summary_time" ); if ( summary_time ) { deleteChildren( summary_time ); if ( summary && summary.time ) { var time = summary.time; if ( time ) { summary_time.appendChild( document.createTextNode( time.toFixed( 2 ) + " seconds" ) ); } // Search progress var search_progress = summary.progress; if ( search_progress ) { summary_time.appendChild( document.createTextNode( " (searched " + (parseFloat( search_progress.firstChild.nodeValue )*100.0).toFixed( 2 ) + "% of Medline)" ) ); } } } // query if ( init ) { var summary_query = $( "results_submitted_query" ); if ( summary_query ) { var query = this.beautifyQuery( this.submittedQuery ); var summary_query_value = $( "results_submitted_query_value" ); if ( summary_query_value ) { deleteChildren( summary_query_value ); var proxy = this; summary_query_value.onclick = function() { proxy.editGCLQuery(); }; summary_query_value.appendChild( document.createTextNode( query )); //summary_query_value.innerHTML = query; } } } }, this.beautifyQuery = function( query ) { debug( "beautifyQuery:" ); var ind = ""; var inds = []; var res; // indent parentheses query = query.replace( /([^()]*?)\s*([()])(\2*)/gm, function ( whole, nonbraces, brace, morebraces ) { if ( brace == "(" ) { if ( nonbraces.length == 1 ) { // operator res = nonbraces + " " + brace; inds.push( false ); } else { // subexpression res = nonbraces + "\n" + ind + brace; inds.push( true ); } ind += " "; } else { res = nonbraces + brace + morebraces; for ( var k = morebraces.length; k >= 0; k-- ) { ind = ind.substring( 0, ind.length - 3 ); if ( inds.pop() ) { res += "\n" + ind; } } } return res; } ); // break up two [...] arguments query = query.replace( /\n(.*)(\[[^\]]*)\]\s\[/g, function ( whole, leader, content ) { ind = leader.replace(/./g, ' '); return "\n" + leader + content + "]\n" + ind + "["; } ); // break up (...) [...] arguments query = query.replace( /\n(.*)(\([^\)]*)\)\s\[/g, function ( whole, leader, content ) { ind = leader.replace(/./g, ' '); return "\n" + leader + content + ")\n" + ind + "["; } ); // remove empty lines query = query.replace( /\n\s*(\n|$)/gm, "\n" ); return query; }, this.initDisplay = function() { var ssroot = $( "sentence_results" ); var saroot = $( "article_results" ); var stroot = $( "table_results" ); hideLayer( "sentence_results" ); hideLayer( "article_results" ); hideLayer( "table_results" ); deleteChildren( ssroot ); deleteChildren( saroot ); deleteChildren( stroot ); if (this.viewOptions.outputFormat == "sentence" ) showLayer( "sentence_results" ); if (this.viewOptions.outputFormat == "article" ) showLayer( "article_results" ); if (this.viewOptions.outputFormat == "table" ) showLayer( "table_results" ); if ( this.displayPosition.start >= this.results.length ) return; var results_table = document.createElement( "table" ); results_table.border = 1; results_table.className = "result_table"; results_table.id = "result_table"; var tr = document.createElement( "tr" ); var th = document.createElement( "th" ); th.appendChild( document.createTextNode( "title" ) ); tr.appendChild( th ); for ( var i = 0; i < this.targetVariables.length; ++i ) { var target = this.targetVariables[ i ]; var td = document.createElement( "th" ); td.className = target; var button1 = document.createElement( "input" ); button1.type = "button"; button1.title = "Sort by " + this.targetVariables[ i ]; var sorttable1 = "sortTable('result_table'," + ( i + 1 ) + ",false)"; button1.onclick = new Function( "", sorttable1 ); button1.value = this.targetVariables[ i ]; var button2 = document.createElement( "input" ); button2.type = "button"; button2.title = "Sort by entities in " + this.targetVariables[ i ]; var sorttable2 = "sortTable('result_table'," + ( i + 1 ) + ",true)"; button2.onclick = new Function( "", sorttable2 ); button2.value = "entities"; td.appendChild( button1 ); td.appendChild( button2 ); tr.appendChild( td ); } var thead = document.createElement( "thead" ); thead.appendChild( tr ); results_table.appendChild( thead ); this.resultsWindow.table = document.createElement( "tbody" ); results_table.appendChild( this.resultsWindow.table ); stroot.appendChild( results_table ); this.resultsWindow.sentence = document.createElement( "table" ); this.resultsWindow.article = document.createElement( "table" ); ssroot.appendChild( this.resultsWindow.sentence ); saroot.appendChild( this.resultsWindow.article ); }, this.showNext = function( start ) { this.displayPosition.start = start; this.displayPosition.end = this.displayPosition.start; this.resultsWindow.sentence = null; this.resultsWindow.article = null; this.resultsWindow.table = null; this.displayResults( false ); }, this.initRequest = function() { if ( this.runGCLRequest == null ) { this.runGCLRequest = createXMLHttpRequest(); } else { this.runGCLRequest.onreadystatechange = function () {}; this.runGCLRequest.abort(); this.runGCLRequest = createXMLHttpRequest(); // hack for mozilla's bug } }, this.initSearch = function() { this.initRequest(); this.gclOptions = new Array(); this.formData = new Array(); var form = document.forms[ "search" ]; for ( var i = 0; i < form.elements.length; ++i ) { var elem = form.elements[ i ]; var valid = false; switch ( elem.type ) { case "checkbox" : case "radio" : valid = elem.checked; break; case "option" : valid = elem.selected; break; case "select-one": case "text" : case "textarea" : case "hidden" : valid = true; } if ( valid ) { this.gclOptions[ elem.name ] = elem.value; this.formData.push( { name: elem.name, value: elem.value } ); } } this.displayPosition = { start: 0, end: 0 }; this.isSearchFinished = null; this.resultsWindow.sentence = null; this.resultsWindow.article = null; this.resultsWindow.table = null; this.targetVariables = null; this.searchPosition = null; this.time = 0; this.submittedQuery = ""; this.results = new Array(); this.summary = new Array(); this.summaryStrings = new Array(); this.sortperm = new Array(); this.current_sort = false; this.setSortEnabled( false ); }, this.runAgain = function() { this.initRequest(); var postData = new String(); postData = "num_results=" + encodeURIComponent( String( this.viewOptions.numberOfResults ) ); var query = this.submittedQuery; postData += "&decross=1"; postData += "&query=" + encodeURIComponent( query ); for ( var i = 0; i < this.summaryStrings.length; ++i ) { postData += "&summary=" + encodeURIComponent( this.summaryStrings[ i ] ); } for ( var i = 0; i < arguments.length; i += 2 ) { postData += "&" + arguments[ i ] + "=" + encodeURIComponent( arguments[ i + 1 ] ); } var proxy = this; this.runGCLRequest.onreadystatechange = function () { proxy.putResults(); }; this.runGCLRequest.open( "POST", rungcl_cgi_name, true ); this.runGCLRequest.setRequestHeader( "Content-Type", "application/x-www-form-urlencoded" ); this.runGCLRequest.send( postData ); }, this.putQuery = function() { // call-back function if ( this.runGCLRequest && this.runGCLRequest.readyState == 4 ) { var addr = '' + document.location.pathname; var re = new RegExp('[^/]+$'); addr = addr.replace(re, query_cgi_name); pageTracker._trackPageview(addr); if ( ! ( this.runGCLRequest.responseText && this.runGCLRequest.status == 200 ) ) { this.displayError( "Disconnected from query server." ); } else if ( ! ( this.runGCLRequest.responseXML && this.runGCLRequest.responseXML.documentElement ) ) { this.displayError( "Query server returned non-XML text." ); } else { var xml = this.runGCLRequest.responseXML.documentElement; this.runGCLRequest = null; var error = xml.getElementsByTagName( "error" )[ 0 ]; if ( error ) { this.displayError( error.firstChild.nodeValue ); return; } var query = xml.getElementsByTagName( "gcl_query" )[ 0 ]; if ( ( ! query ) || ( ! query.firstChild ) || query.firstChild.nodeValue == "" ) { this.displayError( "Empty query." ); return; } this.submittedQuery = query.firstChild.nodeValue; var summary = xml.getElementsByTagName( "summary" ); for ( var i = 0; i < summary.length; ++i ) { if ( summary[ i ].firstChild && summary[ i ].firstChild.nodeValue ) { this.summaryStrings.push( summary[ i ].firstChild.nodeValue ); } } var targets = xml.getElementsByTagName( "target" ); this.targetVariables = new Array( targets.length ); for ( var i = 0; i < targets.length; ++i ) { this.targetVariables[ i ] = targets[ i ].firstChild.nodeValue; } this.displayResults( true ); } } }, this.runGCL = function() { this.initSearch(); // make post data var postData = new String(); postData = "num_results=" + encodeURIComponent( String( NUM_PREFETCH_RESULTS ) ); for ( var i = 0; i < this.formData.length; ++i ) { postData += "&" + this.formData[ i ].name + "=" + encodeURIComponent( this.formData[ i ].value ); } for ( var i = 0; i < arguments.length; i += 2 ) { postData += "&" + arguments[ i ] + "=" + encodeURIComponent( arguments[ i + 1 ] ); } if ( oc.lastResult2 != "" ) { postData += "&cobject=" + encodeURIComponent( oc.lastResult2 ); } if ( sc.lastResult2 != "" ) { postData += "&csubject=" + encodeURIComponent( sc.lastResult2 ); } if ( vc.lastResult2 != "" ) { postData += "&cverb=" + encodeURIComponent( vc.lastResult2 ); } // make a query var proxy = this; this.runGCLRequest.onreadystatechange = function() { proxy.putQuery(); } this.runGCLRequest.open( "POST", query_cgi_name, true ); this.runGCLRequest.setRequestHeader( "Content-Type", "application/x-www-form-urlencoded" ); this.runGCLRequest.send( postData ); }, this.putResults = function() { // call-back function if ( this.runGCLRequest && this.runGCLRequest.readyState == 4 ) { if ( this.runGCLRequest.status == 0) { // Dummy value on Gecko browsers - ignore } else if ( ! ( this.runGCLRequest.responseText && this.runGCLRequest.status == 200 ) ) { this.displayError( "Disconnected from data server." ); } else if ( ! ( this.runGCLRequest.responseXML && this.runGCLRequest.responseXML.documentElement ) ) { this.displayError( "Data server returned Non-XML text." ); } else { var xml = this.runGCLRequest.responseXML.documentElement; this.runGCLRequest = null; var summary = this.createSummary( xml ); var results = xml.getElementsByTagName( "result" ); if ( results.length == 0 ) { this.isSearchFinished = summary; } else { for ( var i = 0; i < results.length; ++i ) { this.results.push( results[ i ] ); this.summary.push( summary ); } } this.current_sort = false; this.setSortEnabled( true ); this.displayResults( false ); } } }, this.createSummary = function( xml ) { var nextPosition = xml.getElementsByTagName( "next" )[ 0 ]; if ( nextPosition ) { this.searchPosition = nextPosition.firstChild.nodeValue; } else { this.searchPosition = ""; } var error = xml.getElementsByTagName( "error" )[ 0 ]; var timeout = xml.getElementsByTagName( "timeout" )[ 0 ]; var time = xml.getElementsByTagName( "time" )[ 0 ]; if ( time ) { this.time += parseFloat( time.firstChild.nodeValue ); } var searchProgress = xml.getElementsByTagName( "progress" )[ 0 ]; return { next : nextPosition, error : error, timeout : timeout, time : this.time, progress: searchProgress }; }, this.getDateForSort = function( element ) { var date = element.getElementsByTagName( "PubDate" ); var year, month, day; if (date.length == 0) { date = element.getElementsByTagName( "MedlineDate" ); if (date.length == 0) return 0; date = getTextValue(date[ 0 ]); // MedlineDate var matches = date.match(/(\d{4})(?:.*?(Jan|Feb|Mar|Apr|May|Jun|Jul|Sep|Oct|Nov|Dec))?/); if (!matches) { console.error("PubDate unrecognised format: ", date); // DEBUG return 0; } year = matches[ 1 ]; month = matches[ 2 ]; } else { date = date[ 0 ]; // PubDate year = date.getElementsByTagName( "Year" ); month = date.getElementsByTagName( "Month" ); day = date.getElementsByTagName( "Day" ); year = year.length ? getTextValue(year[ 0 ]) : 0; month = month.length ? getTextValue(month[ 0 ]) : 0; day = day.length ? getTextValue(day[ 0 ]) : 0; } year = year ? parseInt(year) : 0; if ( month ) { month = month.toLowerCase(); if ( months[ month ] ) month = months[ month ]; } else month = 0; day = day ? parseInt(day) : 0; return year * 371 + month * 31 + day; }, this.setSortEnabled = function( val ) { document.getElementById('sort').disabled = !val; } this.checkSortEnabled = function( el ) { if (!this.results || this.results.length <= 1) return; this.setSortEnabled(el.value != this.current_sort); } this.sort = function() { var criterion; var proxy = this; var what; var radio = $('sortby').childNodes; for (var i in radio) { if (radio[i].name == 'sortby') if (radio[i].checked) what = radio[i].value; } if ( what == undefined ) return; var size = this.results.length; var permsize = this.sortperm.length; this.current_sort = what; this.setSortEnabled( false ); // memoise the newly arrived data var el; var rank; for ( var i = permsize; i < size; i++ ) { el = this.results[ i ]; rank = publication_ranks[getTextValue(el.getElementsByTagName( "NlmUniqueID" )[ 0 ])]; if ( !rank ) rank = lowrank; this.sortperm[ i ] = [ i, this.getDateForSort(el), rank, el.getElementsByTagName( "Title" )[ 0 ].textContent ]; } // sort if ( what == 'rank' ) { criterion = function( a, b ) { if ( a[ 2 ] == lowrank && b[ 2 ] == lowrank ) { // ascending title if ( a[ 3 ] > b[ 3 ] ) return 1; if ( a[ 3 ] < b[ 3 ] ) return -1; return 0; } return a[ 2 ] - b[ 2 ]; // ascending rank }; } else if ( what == 'date' ) { criterion = function( a, b ) { return b[ 1 ] - a[ 1 ]; } // descending date } this.sortperm.sort( criterion ); this.showNext( 0 ); } } var searchObject= new Search(); var Multivalue = function( div, attrs, prog, cand ) { // eg. ("object_div") var div = $(div); var children = div.childNodes; this.field_add = function() { var proxy = this; var size = children.length; if (size > 0) { children[size - 1].childNodes[1].value = 'Remove'; } var row = document.createElement('div'); var field = document.createElement('input'); for (i in attrs) { field.setAttribute(i, attrs[i]); } field.onkeydown = function(event) { if (!event) event = window.event; var key = event.keyCode; if (key == 13 && this.value != "") { proxy.field_add(); return false; } else if ((key == 8 || key == 46) && this.value == "") { return !proxy.field_try_delete(this, key); } return true; } row.appendChild(field); if (prog) { new Completion(field, prog, cand, this); } var button = document.createElement('input'); button.type = 'button'; button.value = 'Add'; button.onclick = function() { if (this.value == 'Add') { proxy.field_add(); } else { div.removeChild(row); children[children.length - 1].value = 'Add'; } } button.tabIndex = -1; row.appendChild(button); div.appendChild(row); if ($('advanced_search').hasClassName('visible')) { field.focus(); } } this.field_try_delete = function(field, key) { if (children.length > 1) { var row = field.parentNode; var nextFocus; if (!key) { } else if ((key == 8 && children[0] !== row) || (key == 46 && children[children.length - 1] === row)) { nextFocus = row.previousSibling; } else { nextFocus = row.nextSibling; } div.removeChild(field.parentNode); children[children.length - 1].childNodes[1].value = 'Add'; if (key) { nextFocus = nextFocus.childNodes[0]; nextFocus.focus(); nextFocus.select(); } return true; // success } return false; // failure } this.reset = function() { while (children.length > 0) { div.removeChild(children[0]); } this.field_add(); } this.field_add(); } ////////////////////////////////////////////////////////////////////// //// //// Completion //// ////////////////////////////////////////////////////////////////////// // XXX: not used anywhere; delete later (2008.09.27) //var Candidate = function ( type, id, symbol, name, species, db_sites ) { // this.type = type; // this.id = id; // this.symbol = symbol; // this.name = name; // this.species = species; // this.db_sites = db_sites; //} var Completion = function( fid, prog, cand, multi ) { // eg. ("object", "completion.cgi", func) this.program = prog; // server program name such as completion.cgi this.window = null; // completion window, a table element to show candidates this.field = $(fid); // input field such as "object" this.toCandidate = cand; // function to return ... object for candidate this.index = null; // fucused candidate index, null means no focus this.last = " "; // last-time string in the field this.passEvent = null; // whether or not to process event after onkeypress this.lastResult2 = ""; // last-time completion result(hidden) such as #GDM01709 for query.cgi use this.focused = false;// whether this.field has the focus this.multi = multi; // a Multivalue object, if used var isJournalTitle = this.field.name == "journal_title"; // methods this.clear = function() { // clear the field this.last = " "; this.lastResult2 = "" this.field.value = ""; }; this.cleanup = function() { // clean up candidates this.index = null; deleteChildren( this.window ); }; this.isShown = function() { // return true if the completion window is shown with candidates if ( this.window && this.window.style.display == "block" && 0 < this.getNumCand() ) { return true; } else { return false; } }; this.hide = function( message ) { // hide the completion window, and cleanup its contents this.window.style.display = "none"; this.cleanup(); }; this.show = function() { // show the completion window var pos = elementPosition( this.field ); this.window.style.top = pos.top + this.field.offsetHeight + "px"; this.window.style.left = pos.left + "px"; this.window.style.visibility = "visible"; this.window.style.display = "block"; }; this.getNumCand = function() { // return number of candidates stored in the window if ( this.window == null ) { return 0; } if ( this.window.childNodes.length == 0 ) { return 0; } return this.window.firstChild.childNodes.length; }; this.setResult = function() { // set result in the field and hide the window if ( this.index == null ) { this.hide( "from setResult 1" ); return; } this.field.value = this.getResult( this.index ); this.lastResult2 = this.getResult2( this.index ); this.index = null; // now, no focus this.hide( "from setResult 2" ); } this.getResult = function( n ) { // return n-th candidate text return this.window.firstChild.childNodes[ n ].firstChild.innerHTML; // table.tbody.tr[n].td[0].innerHTML }; this.getResult2 = function( n ) { // return n-th candidate text, but second element if exists if ( this.window.firstChild.childNodes[n].childNodes.length < 2 ) { return this.getResult( n ); // return first elemtn, table.tbody.tr[n].td[0].innerHTML } else { return this.window.firstChild.childNodes[ n ].childNodes[ 1 ].innerHTML; // table.tbody.tr[n].td[1].innerHTML } }; this.getDecIndex = function() { // get decremented index var number = this.getNumCand(); var n = ( this.index == null )? ( number - 1 ) : ( this.index - 1 ); // TMP // return ( n < 0 )? ( number - 1 ) : n; return ( n < 0 )? null : n; }; this.getIncIndex = function() { // get incremented index var number = this.getNumCand(); var n = ( this.index == null )? 0 : ( this.index + 1 ); // TMP // return ( n >= number )? 0 : n; return ( n >= number )? null : n; }; this.onfocus = function() { this.focused = true; } this.onblur = function() { // when the field lost its focus // onblur deprives event of candidate.onclick .. so, be careful if (multi && this.field.value == "" && multi.field_try_delete(this.field)) { this.hide( "from handleKey/blur" ); } else { this.setResult(); this.focused = false; } }; this.highlight = function ( n ) { // function to highlight the n-th candidate and dehighlight the others var number = this.getNumCand(); for ( var i = 0; i < number; ++i ) { if ( i == n ) { // highlight this.window.firstChild.childNodes[i].style.backgroundColor = color.backgroundSelected; this.window.firstChild.childNodes[i].style.color = color.foregroundSelected; } else { // de-highlight this.window.firstChild.childNodes[i].style.backgroundColor = color.background; this.window.firstChild.childNodes[i].style.color = color.foreground; } } }; this.handleKey = function( event ) { // handle key input if candidates have already been displayed, // this function handles only special inputs such as space or enter // return true/false for further event processing if (!event) event = window.event; var keyCode = ( event.charCode == 32 ) ? 32 : event.keyCode; // for space key handling if (isJournalTitle && keyCode == 32) keyCode = 1032; this.passEvent = false; if (multi && (keyCode == 8 || keyCode == 46) && this.field.value == "" && multi.field_try_delete(this.field, keyCode)) { if (this.request) this.request.canceled = true; this.hide( "from handleKey/delete" ); return false; } if ( ! this.isShown() ) { if ( keyCode == 13 && multi && this.field.value != "" ) { multi.field_add(); return false; } else { // window not shown, quit this.passEvent = true; return true; } } switch ( keyCode ) { case 37: // left key case 38: // up key this.index = this.getDecIndex(); this.highlight( this.index ); return false; // stop further event processing by the browser // XXX: pass tab to the browser and don't execute ajax case 9: // tab key this.passEvent = false; return true; //case 32: // space key case 39: // right key case 40: // down key // TMP //if ( this.isShown() && this.getNumCand() == 1 ) { // special case, only one candidate // this.index = 0; // this.setResult(); // return false; // stop further event processing by the browser // } // else go through this.index = this.getIncIndex(); this.highlight( this.index ); return false; // stop further event processing by the browser case 13: // enter key this.setResult(); if ( multi ) { multi.field_add(); } return false; // stop further event processing by the browser case 27: // escape key this.hide( "from handleKey" ); return false; // stop further event processing by the browser } this.passEvent = true; return true; // keep event processing }; this.onComplete = function( request, key, self ) { // call-back function to display completion var xml = request.responseXML.documentElement; self.cleanup(); // if there is no candidate or the input field has already lost the focus, // hide the completion window and quit if ( key == 13 || xml.childNodes.length == 0 || ! self.focused ) { self.hide( "from onComplete" ); return; } else { self.show(); } // add all candidates to the window var tbody = document.createElement( "tbody" ); var n = xml.childNodes.length; for ( var i = 0; i < n; ++i ) { var candidate = self.toCandidate( xml.childNodes[ i ] ); candidate.className = "" + i; // numbering candidate.onmouseover = function() { // highlight by mouse var number = parseInt( this.className ); self.highlight( number ); self.index = number; }; tbody.appendChild( candidate ); } self.window.appendChild( tbody ); }; this.execute = function( event, text ) { // main function, call this from html(onkeyup) if (!event) event = window.event; if ( ! this.passEvent ) { return; } // handleKey(onkeypress) says no need to execute if ( text == this.last ) { return; } // quit if there is no change in the field // GT 2010-01-21: Try to handle space. Why was it disallowed? // if ( !isJournalTitle && text.indexOf( ' ' ) != -1 ) { // return; // if text contains space, quit, it's vain // } this.last = text; // save the field value this.lastResult2 = ""; // last-time completion cleared var parameter = "query=" + encodeURIComponent( text ); var key = event.keyCode; var self = this; // to use below if (this.request) this.request.canceled = true; new Ajax.Request( this.program, { "method" : "post", "parameters" : parameter, onCreate : function( request ) { self.request = request; }, onComplete : function( request ) { if ( !request.canceled ) self.onComplete( request, key, self ); }, onFailure : function( request ) { alert( "failure" ); }, onException : function( request, exception ) { alert( "Exception: " + exception.message ); } } ); }; // initialization methods this.initWindow = function() { // initial settings for this.window if ( this.window ) { return; } this.window = document.createElement( "table" ); document.body.appendChild( this.window ); this.window.style.position = "absolute"; this.window.cellSpacing = "0px"; this.window.cellPadding = "2px"; this.window.style.borderStyle = "solid"; this.window.style.borderWidth = "1px"; this.window.style.borderColor = color.border; this.window.style.backgroundColor = color.background; this.window.style.padding = "0px"; this.window.style.display = "none"; // or block this.window.style.visibility = "hidden"; // or visible this.window.style.fontSize = "14px"; } var proxy = this; this.field.onkeydown = function(event) { return proxy.handleKey(event); }; this.field.onkeyup = function(event) { return proxy.execute(event, this.value); }; this.field.onfocus = function() { return proxy.onfocus(); }; this.field.onblur = function() { return proxy.onblur(); }; // initialization this.initWindow(); } var titleCandidate = function( c ) { var candidate = document.createElement( "tr" ); var titleString = c.childNodes[ 0 ].firstChild.nodeValue; // ..textContent.nodeValue var title = document.createElement( "td" ); candidate.style.padding = "1px 3px 1px 3px"; title.appendChild( document.createTextNode( titleString ) ); candidate.appendChild( title ) ; return candidate; } var verbCandidate = function( c ) { // c is a <candidate> node var candidate = document.createElement( "tr" ); var verbString = c.childNodes[ 0 ].firstChild.nodeValue; // <candidate>.<verb>.textContent.nodeValue var regulation = c.childNodes[ 1 ].firstChild.nodeValue; // <candidate>.<regulation>.textContent.nodeValue var verb = document.createElement( "td" ); var eventClass = document.createElement( "td" ); candidate.style.padding = "1px 3px 1px 3px"; verb.appendChild( document.createTextNode( verbString ) ); eventClass.appendChild( document.createTextNode( regulation ) ); eventClass.style.display = "none"; candidate.appendChild( verb ) ; candidate.appendChild( eventClass ); return candidate; } // this program is to separate content-dependent parts of the completion system // takes c (<gene>...</gene> xml) // returns a object of <tr> which will be appended to the candidate list in the window var geneCandidate = function( c ) { var candidate = document.createElement( "tr" ); var typeString = c.tagName; var idString = c.childNodes[ 0 ].firstChild.nodeValue; var symbolString = ( c.childNodes[ 1 ].firstChild )? c.childNodes[ 1 ].firstChild.nodeValue : ""; var nameString = ( c.childNodes[ 2 ].firstChild )? c.childNodes[ 2 ].firstChild.nodeValue : ""; var speciesString = ( c.childNodes[ 3 ].firstChild )? c.childNodes[ 3 ].firstChild.nodeValue : ""; var db_sitesString = ( c.childNodes[ 4 ].firstChild )? c.childNodes[ 4 ].firstChild.nodeValue : ""; // 2008-01-29: Disease completion bug fix // var isComplete = ( symbolString == "" )? false : true ; var isComplete = ( speciesString == "" )? false : true ; var result = document.createElement( "td" ); // resultant text for completion such as nrp-7 var result2 = document.createElement( "td" ); // resultant text for completion (hidden) such as GDM150967 var type = document.createElement( "td" ); var symbol = document.createElement( "td" ); var name = document.createElement( "td" ); var species = document.createElement( "td" ); var id = document.createElement( "td" ); candidate.style.padding = "1px 3px 1px 3px"; // hidden field, this content is used for final substitution result.appendChild ( document.createTextNode( symbolString ) ); result2.appendChild ( document.createTextNode( idString ) ); result.style.display = "none"; result2.style.display = "none"; candidate.appendChild( result ) ; candidate.appendChild( result2 ) ; if ( isComplete ) { type.appendChild ( document.createTextNode( typeString + " " ) ); symbol.appendChild ( document.createTextNode( symbolString + " " ) ); name.appendChild ( document.createTextNode( nameString + " " ) ); species.appendChild( document.createTextNode( speciesString + " " ) ); id.appendChild ( document.createTextNode( idString + " " ) ); species.className = dblink_class_map[ speciesString ] + "x" ; type.style.color = color.type; id.style.color = color.id; candidate.appendChild( type ) ; candidate.appendChild( symbol ) ; candidate.appendChild( species ) ; candidate.appendChild( name ) ; } else { type.appendChild ( document.createTextNode( typeString + " " ) ); symbol.appendChild ( document.createTextNode( symbolString + " " ) ); id.appendChild ( document.createTextNode( idString + " " ) ); type.style.color = color.type; id.style.color = color.id; candidate.appendChild( type ); candidate.appendChild( symbol ); candidate.appendChild( id ); } return candidate; } ////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////// //// //// "clear" button //// - for clearing all the field even when a page was generated //// by search.cgi with some initial settings (like subject=p53) //// ////////////////////////////////////////////////////////////////////// function initializeInputFields() { // subject, verb, and object $( "subject" ).value = ""; $( "verb" ).value = ""; $( "object" ).value = ""; // ontology checkboxes $( "subject_ontology" ).checked = true; $( "verb_ontology" ).checked = true; $( "object_ontology" ).checked = true; // base-form checkboxes $( "subject_base_form" ).checked = false; $( "verb_base_form" ).checked = true; $( "object_base_form" ).checked = false; // subject category checkboxes $( "subject_category_gene" ).checked = true; $( "subject_category_product" ).checked = true; $( "subject_category_disease" ).checked = true; // object category checkboxes $( "object_category_gene" ).checked = true; $( "object_category_product" ).checked = true; $( "object_category_disease" ).checked = true; // verb modifier -> disabled because the default value of verb_ontology is true $( "verb_modifier" ).value = ""; // meta-document info fields $( "additional_keyword" ).value = ""; $( "journal_author" ).value = ""; titlemv.reset(); meshmv.reset(); $$("#sentence_type_checkboxes input").each(function(el) { el.checked = true; }); $( "pmid" ).value = ""; } function verbModifierChanged(tfMod) { if (tfMod.value != "") { $('verb_ontology').checked = false; } return true; } function verbOntologyRedisplay() { $('verb_ontology_warning').style.display = "none"; $('verb_ontology_checkbox').style.display = "block"; } function verbOntologyChanged(cbOnt) { var tfMod = $('verb_modifier'); if (cbOnt.checked && tfMod.value != "") { $('verb_ontology_checkbox').style.display = "none"; $('verb_ontology_warning').style.display = "block"; tfMod.select(); tfMod.focus(); cbOnt.checked = false; setTimeout('verbOntologyRedisplay()', 2000); } return true; } var oc, sc, vc; var meshmv, titlemv; function onLoadHandler(topPage) { sc = new Completion( "subject", cgi1, geneCandidate ); // completion for subject vc = new Completion( "verb", cgi2, verbCandidate ); // completion for verb oc = new Completion( "object", cgi1, geneCandidate ); // completion for object //new Completion( "keyword", cgi1, geneCandidate ); // completion for keyword //new Completion( "journal_title", cgi3, titleCandidate ); // completion for journal title meshmv = new Multivalue( "mesh_heading_div", { name: "mesh_heading_list", size: 40 } ); titlemv = new Multivalue( "journal_title_div", { name: "journal_title", size: 40 }, cgi3, titleCandidate); initPopups(); if (!topPage) searchObject.runGCL(); }